One assumes that you already have condition code checking within your job so how do you think it would happen differently to how it is done now? The way to bypass steps are many - the simplest is to use the RESTART parameter on the jobcard (which did not happen in your case). If you could put in a conditon code that would bypass step 1 on refeed then next cycle, when the job is refed to start the cycle, the first step will again be bypassed and would continue to do so for ever-and-a-day. You need to design your batch processes so that they can be refed without having to manually interfere with the restart step.
The problem I have is that people can explain things quickly but I can only comprehend slowly.